Fixed PairedEndWriter so that it correctly filters out read pairs with
greater than 5Mb insert size.

Fixed PairedEndWriter to remove all information about its mate (starting
position, etc) if its mate cannot be found (e.g. if it has been removed
from the input BAM file due to a mapping quality filter).

Fixed AbstractPairedEndAlignment to properly set the inferred insert
size when converting to SAMRecord
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git